During my thesis work I cloned a 3.8 kb bluntended Nde1 fragment into
the Sma1 site of M13mp18 without any serios problems. I used both JM109
and DH5alphaF'IQ as hosts. I would not let your cultures overgrow when
harvestiong phage (8-10 hours max) as this is supposed to be when you
get rearrangements (I never saw any). I followed standard protocols for
cloning and harvesting DNA in M13 without any trouble. If you have
problems email me and I will dig out the specifics of the reactions.
good luck
kirk